|
 AMD64 bi installation
|
Joined: Oct 2005
Posts: 206
Forum Member
|
OP
Forum Member
Joined: Oct 2005
Posts: 206 |
I have AMD-64bit mechines with ubuntu installed when i configured charmm with
./install.com gnu large AMD64
Fri Jun 22 18:01:21 CEST 2007
install.com> Directory /media/sdb1/charmcheck/c32b1/build/gnu does not exist. Creating /media/sdb1/charmcheck/c32b1/build/gnu ...
install.com> Phase 1 completed.
install.com> The preprocessor prefx_gnu installed.
install.com> Phase 2 completed.
install.com> Processing CHARMM source on gnu...
install.com> The CHARMM executable /media/sdb1/charmcheck/c32b1/exec/gnu/charmm is NOT produced. Check /media/sdb1/charmcheck/c32b1/build/gnu/gnu.log for installation errors.
install.com> Phase 3 completed.
and the error in gnu.log file has
Conditional keys: REPLICA RGYCONS RXNCOR SASAE SCPISM SGLD SHAPES SHELL SOFTVDW TNPACK TPS TRAVEL Conditional keys: TSM TSALLIS FITCHG SLVSLV LNTAB1 WCA QUANTUM NOGRAPHICS g77 -mcmodel=medium -ffast-math -funroll-loops -march=k8 -fno-globals -Wno-globals -c -O2 univio.f ar rucv /media/sdb1/charmcheck/c32b1/lib/gnu/io.a univio.o a - univio.o /bin/rm -f univio.f /bin/rm -f univio.o ranlib /media/sdb1/charmcheck/c32b1/lib/gnu/io.a io COMPLETED gcc -Dnographics -O -Dgnu -DLINUX -c /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fmalloc_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:104: warning: conflicting types for built-in function ‘malloc’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fsystem_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:145: warning: incompatible implicit declaration of built-in function ‘exit’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘gethdir_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:177: warning: incompatible implicit declaration of built-in function ‘strncpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:183: warning: incompatible implicit declaration of built-in function ‘strlen’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:188: warning: incompatible implicit declaration of built-in function ‘strcpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:188: warning: incompatible implicit declaration of built-in function ‘strlen’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fgetenv_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:232: warning: incompatible implicit declaration of built-in function ‘strcpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:233: warning: incompatible implicit declaration of built-in function ‘strlen’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fputenv_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:272: warning: incompatible implicit declaration of built-in function ‘strcpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:278: warning: incompatible implicit declaration of built-in function ‘exit’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘filcpy_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:317: warning: incompatible implicit declaration of built-in function ‘strncpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘getunamef_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:375: warning: incompatible implicit declaration of built-in function ‘strlen’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:380: warning: incompatible implicit declaration of built-in function ‘strncpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘etime_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:408: error: ‘CLK_TCK’ undeclared (first use in this function) /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:408: error: (Each undeclared identifier is reported only once /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:408: error: for each function it appears in.) /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘loc_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:622: warning: cast from pointer to integer of different size /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘fdate_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:682: warning: incompatible implicit declaration of built-in function ‘strncpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘uninf_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:948: warning: incompatible implicit declaration of built-in function ‘strlen’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:950: warning: incompatible implicit declaration of built-in function ‘strncpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c: In function ‘binarytesthdrr_’: /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:1139: warning: incompatible implicit declaration of built-in function ‘strncpy’ /media/sdb1/charmcheck/c32b1/source/machdep/cstuff.c:1141: warning: incompatible implicit declaration of built-in function ‘strlen’ make: *** [/media/sdb1/charmcheck/c32b1/lib/gnu/machdep.a(cstuff.o)] Error 1
should i need to use 32bit libraries inorder to solve it. could you please advice me the alternative ideas to install in amd64 bit mechines and how could i use the command.
thanks in advance
|
|
|
 Re: AMD64 bi installation
|
Joined: Sep 2003
Posts: 8,522 Likes: 2
Forum Member
|
Forum Member
Joined: Sep 2003
Posts: 8,522 Likes: 2 |
At the very least, you probably need to make sure that gcc and g77 are from the same release version of the GCC suite; try the --version flag for the compilers.
|
|
|
 Re: AMD64 bi installation
|
Joined: Oct 2005
Posts: 206
Forum Member
|
OP
Forum Member
Joined: Oct 2005
Posts: 206 |
I have following compilers in my mechine
gcc --version gcc (GCC) 4.1.1 20070105 (Red Hat 4.1.1-52) Copyright (C) 2006 Free Software Foundation, Inc. This is free software;
g77 --version GNU Fortran (GCC) 3.4.6 20060404 (Red Hat 3.4.6-4) Copyright (C) 2006 Free Software Foundation, Inc.
|
|
|
 Re: AMD64 bi installation
|
Joined: Sep 2003
Posts: 8,522 Likes: 2
Forum Member
|
Forum Member
Joined: Sep 2003
Posts: 8,522 Likes: 2 |
The gcc version mismatch could be a problem; I've not used g77 for CHARMM on 64-bit machines, so I'm not sure how to advise you further.
|
|
|
 Re: AMD64 bi installation
|
Joined: Feb 2004
Posts: 147
Forum Member
|
Forum Member
Joined: Feb 2004
Posts: 147 |
g77 comes from the compatibility package compat-gcc-34-g77. You should install the corresponding gcc compatibility package which is called compat-gcc-34 and modify Makefile.gnu to use gcc34 instead of gcc. However, this combination is quite likely to produce a CHARMM executable which would not be fully functional, f.e. the large memory allocations might fail.
The other possibility is to modify the same Makefile.gnu and change g77 into gfortran, while leaving gcc as is. This is more likely to produce a well behaving executable than g77+gcc34.
|
|
|
 Re: AMD64 bi installation
|
Joined: Oct 2005
Posts: 206
Forum Member
|
OP
Forum Member
Joined: Oct 2005
Posts: 206 |
intel compiler works fine for 64bit mechines
./install.com gnu large ifort AMD64
|
|
|
|
|
|